Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics
2.2. Animals and Sample Collection
2.3. RNA Isolation, Library Preparation, and Sequencing
2.4. Quality Control and Reference Genome Mapping
2.5. lncRNA Identification and Differentially Expression Analysis
2.6. Potential Target Gene Prediction and Networks Construction
2.7. Function Enrichment Analyses
2.8. Quantitative Real-Time PCR Validation of lncRNA and mRNA
3. Results
3.1. Overview of Transcriptome Sequencing Data
3.2. Identification of mRNA and lncRNA in YunShang Black Goat Oviduct Tissue
3.3. Analysis of DEG and DEL Expression Profiles in the Goat Oviduct
3.4. PPI Analysis of the DEGs Related to Prolificacy Trait
3.5. Functional Analysis of the DEGs
3.6. Analysis of the Targeting Relationship between lncRNAs and mRNAs
3.7. Verification of RNA Expression Profiles with Quantitative Real-Time PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Clean Reads | Clean Base (bp) | Length | Q20 (%) | Q30 (%) | GC (%) | Total Mapped (%) |
---|---|---|---|---|---|---|---|
FL-1 | 52,752,779 | 15,825,833,700 | 150 | 98.35 | 94.75 | 51.45 | 97.13 |
FL-2 | 60,824,479 | 18,247,343,700 | 150 | 98.15 | 94.60 | 50.70 | 96.86 |
FL-3 | 53,704,715 | 16,111,414,500 | 150 | 98.20 | 94.60 | 50.10 | 96.86 |
FL-4 | 51,703,403 | 15,511,020,900 | 150 | 98.45 | 95.05 | 50.10 | 97.35 |
FL-5 | 54,659,450 | 16,397,835,000 | 150 | 98.35 | 95.00 | 48.55 | 96.40 |
FH-1 | 56,457,768 | 16,937,330,400 | 150 | 98.50 | 95.25 | 51.15 | 96.90 |
FH-2 | 51,119,834 | 15,335,950,200 | 150 | 98.08 | 94.20 | 50.00 | 96.40 |
FH-3 | 67,474,481 | 20,242,344,300 | 150 | 97.80 | 93.50 | 51.15 | 96.99 |
FH-4 | 52,753,848 | 15,826,154,400 | 150 | 98.25 | 94.40 | 49.25 | 97.18 |
FH-5 | 50,538,996 | 15,161,698,800 | 150 | 98.50 | 95.10 | 51.25 | 97.18 |
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Sun, Z.; Zhang, Z.; Liu, Y.; Ren, C.; He, X.; Jiang, Y.; Ouyang, Y.; Hong, Q.; Chu, M. Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus). Genes 2022, 13, 1031. https://doi.org/10.3390/genes13061031
Sun Z, Zhang Z, Liu Y, Ren C, He X, Jiang Y, Ouyang Y, Hong Q, Chu M. Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus). Genes. 2022; 13(6):1031. https://doi.org/10.3390/genes13061031
Chicago/Turabian StyleSun, Zhipeng, Zijun Zhang, Yufang Liu, Chunhuan Ren, Xiaoyun He, Yanting Jiang, Yina Ouyang, Qionghua Hong, and Mingxing Chu. 2022. "Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus)" Genes 13, no. 6: 1031. https://doi.org/10.3390/genes13061031
APA StyleSun, Z., Zhang, Z., Liu, Y., Ren, C., He, X., Jiang, Y., Ouyang, Y., Hong, Q., & Chu, M. (2022). Integrated Analysis of mRNAs and Long Non-Coding RNAs Expression of Oviduct That Provides Novel Insights into the Prolificacy Mechanism of Goat (Capra hircus). Genes, 13(6), 1031. https://doi.org/10.3390/genes13061031